******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -0700) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= seqs/AT4G25490_peak_sequences.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme seqs/AT4G25490_peak_sequences.fasta -dna -oc out/AT4G25490 -nostatus -time 300 -mod zoops -nmotifs 2 -minw 6 -maxw 50 -objfun classic -revcomp -markov_order 0 -mpi model: mod= zoops nmotifs= 2 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 6 maxw= 50 nsites: minsites= 2 maxsites= 6223 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 1368560 N= 6223 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.297 C 0.203 G 0.203 T 0.297 Background letter frequencies (from file dataset with add-one prior applied): A 0.3 C 0.2 G 0.2 T 0.3 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NWTGTCGGYR MEME-1 width = 10 sites = 6181 llr = 52063 E-value = 2.8e-440 ******************************************************************************** -------------------------------------------------------------------------------- Motif NWTGTCGGYR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 242::::::3 pos.-specific C 212::a::52 probability G 221a::aa:4 matrix T 335:a:::51 bits 2.3 * ** 2.1 * *** 1.9 * *** 1.6 ***** Relative 1.4 ***** Entropy 1.2 ***** (12.2 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ******** 0.0 ---------- Multilevel TATGTCGGCG consensus GTC TA sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NWTGTCGGYR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 1312553 bayes= 9.8295 E= 2.8e-440 -38 -15 28 20 45 -113 -30 17 -77 1 -71 74 -1924 -1924 232 -1924 -827 -769 -710 173 -1924 232 -1924 -1924 -1924 -1924 232 -1924 -307 -1924 227 -1924 -497 133 -1924 70 -1 -39 100 -102 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NWTGTCGGYR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 6181 E= 2.8e-440 0.230383 0.181039 0.243650 0.344928 0.408186 0.091571 0.163080 0.337162 0.175538 0.201747 0.122634 0.500081 0.000000 0.000000 1.000000 0.000000 0.000971 0.000971 0.001456 0.996602 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.035755 0.000000 0.964245 0.000000 0.009545 0.504934 0.000000 0.485520 0.298010 0.153211 0.400744 0.148034 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NWTGTCGGYR MEME-1 regular expression -------------------------------------------------------------------------------- [TGA][AT][TC]GTCGG[CT][GA] -------------------------------------------------------------------------------- Time 73.40 secs. ******************************************************************************** ******************************************************************************** MOTIF ARARRRAGAARRAGARRRAGA MEME-2 width = 21 sites = 2552 llr = 22709 E-value = 4.1e-070 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARARRRAGAARRAGARRRAGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 547546727646838465736 pos.-specific C 2:12111:121:1:11:1111 probability G 262353172253:72344162 matrix T 1::1::21:1:11::1::1:1 bits 2.3 2.1 1.9 1.6 Relative 1.4 Entropy 1.2 (12.8 bits) 0.9 * * * * 0.7 * ** ** ***** **** 0.5 ** ***** ***** ***** 0.2 ********************* 0.0 --------------------- Multilevel AGAAGAAGAAGAAGAAAAAGA consensus A GAG AG AG A GGG AG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARARRRAGAARRAGARRRAGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1244100 bayes= 10.9867 E= 4.1e-070 82 -33 -4 -134 45 -285 149 -1796 115 -110 -3 -267 61 -26 36 -133 40 -155 142 -1796 100 -133 60 -429 116 -99 -135 -99 -38 -1796 179 -196 121 -155 10 -358 93 -19 -32 -168 56 -179 131 -626 98 -491 78 -239 135 -51 -371 -194 -2 -1796 173 -295 133 -155 -34 -385 55 -76 64 -122 94 -335 83 -260 80 -116 96 -1796 131 -99 -160 -170 -16 -79 155 -333 98 -161 27 -157 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARARRRAGAARRAGARRRAGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 2552 E= 4.1e-070 0.527821 0.159091 0.194749 0.118339 0.408307 0.027821 0.563871 0.000000 0.664185 0.093260 0.195533 0.047022 0.457288 0.166928 0.256661 0.119122 0.395768 0.068182 0.536050 0.000000 0.601097 0.079937 0.303683 0.015282 0.669671 0.100705 0.078370 0.151254 0.230799 0.000000 0.692006 0.077194 0.691223 0.068574 0.215125 0.025078 0.570533 0.175940 0.160266 0.093260 0.441614 0.057994 0.496473 0.003918 0.591301 0.006661 0.344828 0.057210 0.766458 0.140282 0.015282 0.077978 0.295455 0.000000 0.665752 0.038793 0.752743 0.068182 0.158307 0.020768 0.440047 0.118339 0.313088 0.128527 0.574060 0.019592 0.356975 0.049373 0.521552 0.089734 0.388715 0.000000 0.740596 0.100705 0.066223 0.092476 0.267633 0.115987 0.586599 0.029781 0.591693 0.065439 0.242163 0.100705 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARARRRAGAARRAGARRRAGA MEME-2 regular expression -------------------------------------------------------------------------------- A[GA]A[AG][GA][AG]A[GA][AG]A[GA][AG]A[GA]A[AG][AG][AG]A[GA][AG] -------------------------------------------------------------------------------- Time 142.55 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************